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I suppose if I was the referee for this structure and your FreeR is so close to the Rfactor I would ask you to ensure you had the right space group - is the 6 fold NCS actually 2 fold NCS with a crystallographic 3 fold.. Cases occur where R32 is indexed as C2.. Certainly if the Rfree set is assigned randomly to reflections which are symmetry equivalents then you see this phenomena of Rfree = Rfactor Eleanor On 30 June 2015 at 18:26, Gerard Bricogne <[log in to unmask]> wrote: > Dear Wolfram, > > I have a perhaps optimistic view of the effect of high-order NCS > on Rfree, in the sense that I don't view it as a "problem". People > have agonised to extreme degrees over the "difficulty" of choosing a > free set of reflections that would produce the expected gap between > Rwork and Rfree, and some of the conclusions were that you would need > to hide almost half of your data in some cases! > > I think it is best to remember that the idea of cross-validation > by Rfree is to prevent overfitting, i.e. ending up with a model that > fits the amplitudes too well compared to how well it determines the > phases. In the case of high-order NCS (in your case, the U/V ratio > that the old papers on NCS identified as the key quantity to measure > the phasing power of NCS would be less than 0.1!) the phases and the > amplitudes are so tightly coupled that it is simply impossible to fit > the amplitudes without delivering phases of an equally good quality. > In other words there is no overfitting problem (provided you do have > good and complete data) and the difference between Rfree and Rwork is > simply within the bounds of the statistical spread of Rfree depending > on the free set chosen. > > You are lucky to have 6-fold NCS, so don't let any reviewer > convince you that it is a curse, and make you suffer for it :-) . > > > With best wishes, > > Gerard. > > -- > On Tue, Jun 30, 2015 at 12:58:44PM -0400, wtempel wrote: > > Hello, > > my question concerns refinement of a structure with 6-fold NCS (local > > automatic restraints in REFMAC) against 2.8 A data. The size of my free > set > > is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to > > 4.3 % of reflections. > > A refmac run of 10 cycles of TLS and 10 cycles of CGMAT starts out at > > Rfree/Rcryst 0.271/0.272. After the 10th TLS cycle I have 0.227/0.224. > Yes, > > Rfree < Rcryst. At the end of CGMAT I have 0.2072/0.2071. > > I understand that NCS stresses the independence assumption of the free > set. > > Am I correct in believing that Rfree *may* be smaller than Rcryst even in > > the absence of a major mistake? My hope is that the combined wisdom of > > ccp4bb followers can point out my possible mistake, suggest tests that I > > may perform to avoid them and, possibly, arguments in defense of a > > crystallographic model with Rfree < Rcryst. > > Many thanks, > > Wolfram Tempel > > -- > > =============================================================== > * * > * Gerard Bricogne [log in to unmask] * > * * > * Global Phasing Ltd. * > * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * > * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * > * * > =============================================================== >